1
|
Gest AMM, Sahan AZ, Zhong Y, Lin W, Mehta S, Zhang J. Molecular Spies in Action: Genetically Encoded Fluorescent Biosensors Light up Cellular Signals. Chem Rev 2024. [PMID: 39535501 DOI: 10.1021/acs.chemrev.4c00293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
Abstract
Cellular function is controlled through intricate networks of signals, which lead to the myriad pathways governing cell fate. Fluorescent biosensors have enabled the study of these signaling pathways in living systems across temporal and spatial scales. Over the years there has been an explosion in the number of fluorescent biosensors, as they have become available for numerous targets, utilized across spectral space, and suited for various imaging techniques. To guide users through this extensive biosensor landscape, we discuss critical aspects of fluorescent proteins for consideration in biosensor development, smart tagging strategies, and the historical and recent biosensors of various types, grouped by target, and with a focus on the design and recent applications of these sensors in living systems.
Collapse
Affiliation(s)
- Anneliese M M Gest
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
| | - Ayse Z Sahan
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California 92093, United States
| | - Yanghao Zhong
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
| | - Wei Lin
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| |
Collapse
|
2
|
Kwak CS, Oflaz FE, Qiu J, Wang X. Human stem cell-specific epigenetic signatures control transgene expression. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195063. [PMID: 39437851 DOI: 10.1016/j.bbagrm.2024.195063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 10/03/2024] [Accepted: 10/12/2024] [Indexed: 10/25/2024]
Abstract
Human stem cell-derived models have emerged as an important platform to study tissue differentiation and disease mechanisms. Those models could capitalize on biochemical and cell biological methodologies such as omics, autophagy, and organelle dynamics. However, epigenetic silencing in stem cells creates a barrier to apply genetically encoded tools. Here we investigate the molecular mechanisms underlying exogenously expressed gene silencing by employing multiple commonly used promoters in human induced pluripotent stem cells (iPSCs), glioblastoma cells (GBM), and embryonic kidney cells (HEK). We discover that all promoters tested are highly methylated on the CpG island regions with lower protein expression in iPSCs, as compared to non-iPSCs. Elongation factor 1 alpha short (EF1α short or EFS) promoter, which has fewer CpG island number compared to the other promoters, can drive relatively higher gene expression in iPSCs, despite CpG methylation. Adding a minimal A2 ubiquitous chromatin opening element (minimal A2 UCOE or miniUCOE) upstream of a promoter inhibits CpG methylation and enhances gene expression in iPSCs. Our results demonstrate stem cell type-specific epigenetic modification of transgenic promoter region and provide useful information for designing anti-silencing strategies to increase transgene expression in iPSCs.
Collapse
Affiliation(s)
- Chulhwan S Kwak
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Furkan E Oflaz
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jiamin Qiu
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xinnan Wang
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
3
|
Ghoochani A, Heiby JC, Rawat ES, Medoh UN, Di Fraia D, Dong W, Gastou M, Nyame K, Laqtom NN, Gomez-Ospina N, Ori A, Abu-Remaileh M. Cell-Type Resolved Protein Atlas of Brain Lysosomes Identifies SLC45A1-Associated Disease as a Lysosomal Disorder. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.14.618295. [PMID: 39464040 PMCID: PMC11507716 DOI: 10.1101/2024.10.14.618295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
Mutations in lysosomal genes cause neurodegeneration and neurological lysosomal storage disorders (LSDs). Despite their essential role in brain homeostasis, the cell-type-specific composition and function of lysosomes remain poorly understood. Here, we report a quantitative protein atlas of the lysosome from mouse neurons, astrocytes, oligodendrocytes, and microglia. We identify dozens of novel lysosomal proteins and reveal the diversity of the lysosomal composition across brain cell types. Notably, we discovered SLC45A1, mutations in which cause a monogenic neurological disease, as a neuron-specific lysosomal protein. Loss of SLC45A1 causes lysosomal dysfunction in vitro and in vivo. Mechanistically, SLC45A1 plays a dual role in lysosomal sugar transport and stabilization of V1 subunits of the V-ATPase. SLC45A1 deficiency depletes the V1 subunits, elevates lysosomal pH, and disrupts iron homeostasis causing mitochondrial dysfunction. Altogether, our work redefines SLC45A1-associated disease as a LSD and establishes a comprehensive map to study lysosome biology at cell-type resolution in the brain and its implications for neurodegeneration.
Collapse
Affiliation(s)
- Ali Ghoochani
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network; Chevy Chase, MD, 20815, USA
- These authors contributed equally
| | - Julia C. Heiby
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) e.V., Jena, Germany
- These authors contributed equally
| | - Eshaan S. Rawat
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network; Chevy Chase, MD, 20815, USA
| | - Uche N. Medoh
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network; Chevy Chase, MD, 20815, USA
- Current affiliation: Arc Institute, Palo Alto, CA 94304, USA
| | - Domenico Di Fraia
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) e.V., Jena, Germany
- Current affiliation: Department of Biology, University of Rochester, Rochester, NY, USA
| | - Wentao Dong
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network; Chevy Chase, MD, 20815, USA
| | - Marc Gastou
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Kwamina Nyame
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network; Chevy Chase, MD, 20815, USA
| | - Nouf N. Laqtom
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network; Chevy Chase, MD, 20815, USA
| | - Natalia Gomez-Ospina
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) e.V., Jena, Germany
- Co-senior authors
| | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network; Chevy Chase, MD, 20815, USA
- The Phil & Penny Knight Initiative for Brain Resilience at the Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
- Co-senior authors
- Lead author
| |
Collapse
|
4
|
Feng T, Zheng H, Zhang Z, Fan P, Yang X. Mechanism and therapeutic targets of the involvement of a novel lysosomal proton channel TMEM175 in Parkinson's disease. Ageing Res Rev 2024; 100:102373. [PMID: 38960046 DOI: 10.1016/j.arr.2024.102373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 07/05/2024]
Abstract
Parkinson's disease (PD), recognized as the second most prevalent neurodegenerative disease in the aging population, presents a significant challenge due to the current lack of effective treatment methods to mitigate its progression. Many pathogenesis of PD are related to lysosomal dysfunction. Moreover, extensive genetic studies have shown a significant correlation between the lysosomal membrane protein TMEM175 and the risk of developing PD. Building on this discovery, TMEM175 has been identified as a novel potassium ion channel. Intriguingly, further investigations have found that potassium ion channels gradually close and transform into hydrion "excretion" channels in the microenvironment of lysosomes. This finding was further substantiated by studies on TMEM175 knockout mice, which exhibited pronounced motor dysfunction in pole climbing and suspension tests, alongside a notable reduction in dopamine neurons within the substantia nigra compacta. Despite these advancements, the current research landscape is not without its controversies. In light of this, the present review endeavors to methodically examine and consolidate a vast array of recent literature on TMEM175. This comprehensive analysis spans from the foundational research on the structure and function of TMEM175 to expansive population genetics studies and mechanism research utilizing cellular and animal models.A thorough understanding of the structure and function of TMEM175, coupled with insights into the intricate mechanisms underpinning lysosomal dysfunction in PD dopaminergic neurons, is imperative. Such knowledge is crucial for pinpointing precise intervention targets, thereby paving the way for novel therapeutic strategies that could potentially alter the neurodegenerative trajectory of PD.
Collapse
Affiliation(s)
- Tingting Feng
- Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumqi 830063, China; Xinjiang Key Laboratory of Nervous System Disease Research, Urumqi 830063,China; Xinjiang Clinical Research Center for Nervous System Diseases, Urumqi 830063, China; Xinjiang Medical University, Urumqi 830017, China
| | | | - Zhan Zhang
- Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumqi 830063, China; Xinjiang Key Laboratory of Nervous System Disease Research, Urumqi 830063,China; Xinjiang Clinical Research Center for Nervous System Diseases, Urumqi 830063, China
| | - Peidong Fan
- Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumqi 830063, China; Xinjiang Key Laboratory of Nervous System Disease Research, Urumqi 830063,China; Xinjiang Clinical Research Center for Nervous System Diseases, Urumqi 830063, China
| | - Xinling Yang
- Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumqi 830063, China; Xinjiang Key Laboratory of Nervous System Disease Research, Urumqi 830063,China; Xinjiang Clinical Research Center for Nervous System Diseases, Urumqi 830063, China; Xinjiang Medical University, Urumqi 830017, China.
| |
Collapse
|
5
|
Leng K, Rooney B, McCarthy F, Xia W, Rose IVL, Bax S, Chin M, Fathi S, Herrington KA, Leonetti M, Kao A, Fancy SPJ, Elias JE, Kampmann M. mTOR activation induces endolysosomal remodeling and nonclassical secretion of IL-32 via exosomes in inflammatory reactive astrocytes. J Neuroinflammation 2024; 21:198. [PMID: 39118084 PMCID: PMC11312292 DOI: 10.1186/s12974-024-03165-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 07/03/2024] [Indexed: 08/10/2024] Open
Abstract
Astrocytes respond and contribute to neuroinflammation by adopting inflammatory reactive states. Although recent efforts have characterized the gene expression signatures associated with these reactive states, the cell biology underlying inflammatory reactive astrocyte phenotypes remains under-explored. Here, we used CRISPR-based screening in human iPSC-derived astrocytes to identify mTOR activation a driver of cytokine-induced endolysosomal system remodeling, manifesting as alkalinization of endolysosomal compartments, decreased autophagic flux, and increased exocytosis of certain endolysosomal cargos. Through endolysosomal proteomics, we identified and focused on one such cargo-IL-32, a disease-associated pro-inflammatory cytokine not present in rodents, whose secretion mechanism is not well understood. We found that IL-32 was partially secreted in extracellular vesicles likely to be exosomes. Furthermore, we found that IL-32 was involved in the polarization of inflammatory reactive astrocyte states and was upregulated in astrocytes in multiple sclerosis lesions. We believe that our results advance our understanding of cell biological pathways underlying inflammatory reactive astrocyte phenotypes and identify potential therapeutic targets.
Collapse
Affiliation(s)
- Kun Leng
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA.
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA.
| | - Brendan Rooney
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | | | - Wenlong Xia
- Departments of Neurology and Pediatrics, School of Medicine, University of California, San Francisco, CA, USA
| | - Indigo V L Rose
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Sophie Bax
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Marcus Chin
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Small Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Saeed Fathi
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
| | - Kari A Herrington
- Center for Advanced Microscopy, University of California, San Francisco, San Francisco, CA, USA
| | | | - Aimee Kao
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen P J Fancy
- Departments of Neurology and Pediatrics, School of Medicine, University of California, San Francisco, CA, USA
| | | | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA.
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
6
|
Bhat M, Nambiar A, Edakkandiyil L, Abraham IM, Sen R, Negi M, Manjithaya R. A genetically-encoded fluorescence-based reporter to spatiotemporally investigate mannose-6-phosphate pathway. Mol Biol Cell 2024; 35:mr6. [PMID: 38888935 PMCID: PMC11321044 DOI: 10.1091/mbc.e23-09-0344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 06/04/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024] Open
Abstract
Maintenance of a pool of active lysosomes with acidic pH and degradative hydrolases is crucial for cell health. Abnormalities in lysosomal function are closely linked to diseases, such as lysosomal storage disorders, neurodegeneration, intracellular infections, and cancer among others. Emerging body of research suggests the malfunction of lysosomal hydrolase trafficking pathway to be a common denominator of several disease pathologies. However, available conventional tools to assess lysosomal hydrolase trafficking are insufficient and fail to provide a comprehensive picture about the trafficking flux and location of lysosomal hydrolases. To address some of the shortcomings, we designed a genetically-encoded fluorescent reporter containing a lysosomal hydrolase tandemly tagged with pH sensitive and insensitive fluorescent proteins, which can spatiotemporally trace the trafficking of lysosomal hydrolases. As a proof of principle, we demonstrate that the reporter can detect perturbations in hydrolase trafficking, that are induced by pharmacological manipulations and pathophysiological conditions like intracellular protein aggregates. This reporter can effectively serve as a probe for mapping the mechanistic intricacies of hydrolase trafficking pathway in health and disease and is a utilitarian tool to identify genetic and pharmacological modulators of this pathway, with potential therapeutic implications.
Collapse
Affiliation(s)
- Mallika Bhat
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Akshaya Nambiar
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | | | - Irine Maria Abraham
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Ritoprova Sen
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Mamta Negi
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Ravi Manjithaya
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
- Professor and chair, Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| |
Collapse
|
7
|
Bretou M, Sannerud R, Escamilla-Ayala A, Leroy T, Vrancx C, Van Acker ZP, Perdok A, Vermeire W, Vorsters I, Van Keymolen S, Maxson M, Pavie B, Wierda K, Eskelinen EL, Annaert W. Accumulation of APP C-terminal fragments causes endolysosomal dysfunction through the dysregulation of late endosome to lysosome-ER contact sites. Dev Cell 2024; 59:1571-1592.e9. [PMID: 38626765 DOI: 10.1016/j.devcel.2024.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/02/2023] [Accepted: 03/20/2024] [Indexed: 04/18/2024]
Abstract
Neuronal endosomal and lysosomal abnormalities are among the early changes observed in Alzheimer's disease (AD) before plaques appear. However, it is unclear whether distinct endolysosomal defects are temporally organized and how altered γ-secretase function or amyloid precursor protein (APP) metabolism contribute to these changes. Inhibiting γ-secretase chronically, in mouse embryonic fibroblast and hippocampal neurons, led to a gradual endolysosomal collapse initiated by decreased lysosomal calcium and increased cholesterol, causing downstream defects in endosomal recycling and maturation. This endolysosomal demise is γ-secretase dependent, requires membrane-tethered APP cytoplasmic domains, and is rescued by APP depletion. APP C-terminal fragments (CTFs) localized to late endosome/lysosome-endoplasmic reticulum contacts; an excess of APP-CTFs herein reduced lysosomal Ca2+ refilling from the endoplasmic reticulum, promoting cholesterol accretion. Tonic regulation by APP-CTFs provides a mechanistic explanation for their cellular toxicity: failure to timely degrade APP-CTFs sustains downstream signaling, instigating lysosomal dyshomeostasis, as observed in prodromal AD. This is the opposite of substrates such as Notch, which require intramembrane proteolysis to initiate signaling.
Collapse
Affiliation(s)
- Marine Bretou
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Ragna Sannerud
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | | | - Tom Leroy
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Céline Vrancx
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Zoë P Van Acker
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Anika Perdok
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Wendy Vermeire
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Inge Vorsters
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Sophie Van Keymolen
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Michelle Maxson
- Cell Biology Program, The Hospital for Sick Children, Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Benjamin Pavie
- VIB-BioImaging Core, VIB-Center for Brain and Disease Research, Leuven, Belgium
| | - Keimpe Wierda
- Electrophysiology Expertise Unit, VIB-Center for Brain and Disease Research, Leuven, Belgium
| | | | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium.
| |
Collapse
|
8
|
Tyagi A, Mir ZA, Ali S. Revisiting the Role of Sensors for Shaping Plant Research: Applications and Future Perspectives. SENSORS (BASEL, SWITZERLAND) 2024; 24:3261. [PMID: 38894052 PMCID: PMC11174810 DOI: 10.3390/s24113261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/14/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024]
Abstract
Plant health monitoring is essential for understanding the impact of environmental stressors (biotic and abiotic) on crop production, and for tailoring plant developmental and adaptive responses accordingly. Plants are constantly exposed to different stressors like pathogens and soil pollutants (heavy metals and pesticides) which pose a serious threat to their survival and to human health. Plants have the ability to respond to environmental stressors by undergoing rapid transcriptional, translational, and metabolic reprogramming at different cellular compartments in order to balance growth and adaptive responses. However, plants' exceptional responsiveness to environmental cues is highly complex, which is driven by diverse signaling molecules such as calcium Ca2+, reactive oxygen species (ROS), hormones, small peptides and metabolites. Additionally, other factors like pH also influence these responses. The regulation and occurrence of these plant signaling molecules are often undetectable, necessitating nondestructive, live research approaches to understand their molecular complexity and functional traits during growth and stress conditions. With the advent of sensors, in vivo and in vitro understanding of some of these processes associated with plant physiology, signaling, metabolism, and development has provided a novel platform not only for decoding the biochemical complexity of signaling pathways but also for targeted engineering to improve diverse plant traits. The application of sensors in detecting pathogens and soil pollutants like heavy metal and pesticides plays a key role in protecting plant and human health. In this review, we provide an update on sensors used in plant biology for the detection of diverse signaling molecules and their functional attributes. We also discuss different types of sensors (biosensors and nanosensors) used in agriculture for detecting pesticides, pathogens and pollutants.
Collapse
Affiliation(s)
- Anshika Tyagi
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Zahoor Ahmad Mir
- Department of Plant Science and Agriculture, University of Manitoba, Winnipeg, MB R2M0TB, Canada;
| | - Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
| |
Collapse
|
9
|
Yin Q, Yang C. Exploring lysosomal biology: current approaches and methods. BIOPHYSICS REPORTS 2024; 10:111-120. [PMID: 38774350 PMCID: PMC11103719 DOI: 10.52601/bpr.2023.230028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 01/04/2024] [Indexed: 05/24/2024] Open
Abstract
Lysosomes are the degradation centers and signaling hubs in the cell. Lysosomes undergo adaptation to maintain cell homeostasis in response to a wide variety of cues. Dysfunction of lysosomes leads to aging and severe diseases including lysosomal storage diseases (LSDs), neurodegenerative disorders, and cancer. To understand the complexity of lysosome biology, many research approaches and tools have been developed to investigate lysosomal functions and regulatory mechanisms in diverse experimental systems. This review summarizes the current approaches and tools adopted for studying lysosomes, and aims to provide a methodological overview of lysosomal research and related fields.
Collapse
Affiliation(s)
- Qiuyuan Yin
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Chonglin Yang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650091, China
- Southwest United Graduate School, Kunming 650092, China
| |
Collapse
|
10
|
Bond C, Hugelier S, Xing J, Sorokina EM, Lakadamyali M. Multiplexed DNA-PAINT Imaging of the Heterogeneity of Late Endosome/Lysosome Protein Composition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585634. [PMID: 38562776 PMCID: PMC10983937 DOI: 10.1101/2024.03.18.585634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Late endosomes/lysosomes (LELs) are crucial for numerous physiological processes and their dysfunction is linked to many diseases. Proteomic analyses have identified hundreds of LEL proteins, however, whether these proteins are uniformly present on each LEL, or if there are cell-type dependent LEL sub-populations with unique protein compositions is unclear. We employed a quantitative, multiplexed DNA-PAINT super-resolution approach to examine the distribution of six key LEL proteins (LAMP1, LAMP2, CD63, TMEM192, NPC1 and LAMTOR4) on individual LELs. While LAMP1 and LAMP2 were abundant across LELs, marking a common population, most analyzed proteins were associated with specific LEL subpopulations. Our multiplexed imaging approach identified up to eight different LEL subpopulations based on their unique membrane protein composition. Additionally, our analysis of the spatial relationships between these subpopulations and mitochondria revealed a cell-type specific tendency for NPC1-positive LELs to be closely positioned to mitochondria. Our approach will be broadly applicable to determining organelle heterogeneity with single organelle resolution in many biological contexts. Summary This study develops a multiplexed and quantitative DNA-PAINT super-resolution imaging pipeline to investigate the distribution of late endosomal/lysosomal (LEL) proteins across individual LELs, revealing cell-type specific LEL sub-populations with unique protein compositions, offering insights into organelle heterogeneity at single-organelle resolution.
Collapse
|
11
|
Tsytsarev V, Sopova JV, Leonova EI, Inyushin M, Markina AA, Chirinskaite AV, Volnova AB. Neurophotonic methods in approach to in vivo animal epileptic models: Advantages and limitations. Epilepsia 2024; 65:600-614. [PMID: 38115808 PMCID: PMC10948300 DOI: 10.1111/epi.17870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023]
Abstract
Neurophotonic technology is a rapidly growing group of techniques that are based on the interactions of light with natural or genetically modified cells of the neural system. New optical technologies make it possible to considerably extend the tools of neurophysiological research, from the visualization of functional activity changes to control of brain tissue excitability. This opens new perspectives for studying the mechanisms underlying the development of human neurological diseases. Epilepsy is one of the most common brain disorders; it is characterized by recurrent seizures and affects >1% of the world's population. However, how seizures occur, spread, and terminate in a healthy brain is still unclear. Therefore, it is extremely important to develop appropriate models to accurately explore the causal relationship of epileptic activity. The use of neurophotonic technologies in epilepsy research falls into two broad categories: the visualization of neural epileptic activity, and the direct optical influence on neurons to induce or suppress epileptic activity. An optogenetic variant of the classical kindling model of epileptic seizures, in which activatable cells are genetically defined, is called optokindling. Research is also underway concerning the application of neurophotonic techniques for suppressing epileptic activity, aiming to bring these methods into clinical practice. This review aims to systematize and describe new approaches that use combinations of different neurophotonic methods to work with in vivo models of epilepsy. These approaches overcome many of the shortcomings associated with classical animal models of epilepsy and thus increase the effectiveness of developing new diagnostic methods and antiepileptic therapy.
Collapse
Affiliation(s)
- Vassiliy Tsytsarev
- University of Maryland School of Medicine, Department of Neurobiology 20 Penn St, HSF-2, 21201 MD, Baltimore, United States
| | - Julia V. Sopova
- Center of Transgenesis and Genome Editing, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Elena I. Leonova
- Center of Transgenesis and Genome Editing, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Mikhail Inyushin
- School of Medicine, Universidad Central del Caribe, Bayamon, PR 00956, USA
| | - Alisa A. Markina
- Institute of Translational Biomedicine, Saint Petersburg State University, St. Petersburg 199034, Russia
| | - Angelina V. Chirinskaite
- Center of Transgenesis and Genome Editing, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna B. Volnova
- Institute of Translational Biomedicine, Saint Petersburg State University, St. Petersburg 199034, Russia
| |
Collapse
|
12
|
Ma J, Lu X, Hao M, Wang Y, Guo Y, Wang Z. Real-time visualization the pH fluctuations of living cells with a ratiometric near-infrared fluorescent probe. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 306:123572. [PMID: 37922853 DOI: 10.1016/j.saa.2023.123572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/18/2023] [Accepted: 10/21/2023] [Indexed: 11/07/2023]
Abstract
In situ real-time quantitative monitoring pH fluctuation in complex living systems is vitally significant. In the current work, a ratiometric near-infrared (NIR) probe (MCyOH) was developed to confront this challenge. MCyOH exhibited good sensitivity, photostability, reversibility, and an ideal pKa (pKa = 6.65). Ratiometric character of MCyOH is beneficial to accuracy detect the pH fluctuations in living cells under different stimulation. The observations showed that intracellular pH was decreased when HepG2 cells under oxidative stress or starvation conditions. In particular, HepG2 cells was acidulated after addition of ethanol, however, the acidification phenomenon was attenuated or disappeared when HepG2 cells preincubated with disulfiram or fomepizole. Finally, MCyOH was successfully applied to observe the increasement of intracellular pH when HepG2 cells treated with fomepizole individually. Overall, MCyOH would be a practical candidate to explore pH-associated physiological and pathological varieties.
Collapse
Affiliation(s)
- Jianlong Ma
- Department of Chemistry, Changzhi University, Changzhi 046011, PR China; Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, Gansu 730000, PR China
| | - Xiaofeng Lu
- Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, Gansu 730000, PR China
| | - Mingyao Hao
- Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, Gansu 730000, PR China; University of Chinese Academy of Sciences, 100049 Beijing, PR China
| | - Yumeng Wang
- Department of Chemistry, Changzhi University, Changzhi 046011, PR China
| | - Yong Guo
- Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, Gansu 730000, PR China.
| | - Zhijun Wang
- Department of Chemistry, Changzhi University, Changzhi 046011, PR China.
| |
Collapse
|
13
|
Li SA, Meng XY, Zhang YJ, Chen CL, Jiao YX, Zhu YQ, Liu PP, Sun W. Progress in pH-Sensitive sensors: essential tools for organelle pH detection, spotlighting mitochondrion and diverse applications. Front Pharmacol 2024; 14:1339518. [PMID: 38269286 PMCID: PMC10806205 DOI: 10.3389/fphar.2023.1339518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024] Open
Abstract
pH-sensitive fluorescent proteins have revolutionized the field of cellular imaging and physiology, offering insight into the dynamic pH changes that underlie fundamental cellular processes. This comprehensive review explores the diverse applications and recent advances in the use of pH-sensitive fluorescent proteins. These remarkable tools enable researchers to visualize and monitor pH variations within subcellular compartments, especially mitochondria, shedding light on organelle-specific pH regulation. They play pivotal roles in visualizing exocytosis and endocytosis events in synaptic transmission, monitoring cell death and apoptosis, and understanding drug effects and disease progression. Recent advancements have led to improved photostability, pH specificity, and subcellular targeting, enhancing their utility. Techniques for multiplexed imaging, three-dimensional visualization, and super-resolution microscopy are expanding the horizon of pH-sensitive protein applications. The future holds promise for their integration into optogenetics and drug discovery. With their ever-evolving capabilities, pH-sensitive fluorescent proteins remain indispensable tools for unravelling cellular dynamics and driving breakthroughs in biological research. This review serves as a comprehensive resource for researchers seeking to harness the potential of pH-sensitive fluorescent proteins.
Collapse
Affiliation(s)
- Shu-Ang Li
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiao-Yan Meng
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ying-Jie Zhang
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Cai-Li Chen
- Department of Immunology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yu-Xue Jiao
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yong-Qing Zhu
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Pei-Pei Liu
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Sun
- Department of Burn and Repair Reconstruction, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
14
|
Posner C, Mehta S, Zhang J. Fluorescent biosensor imaging meets deterministic mathematical modelling: quantitative investigation of signalling compartmentalization. J Physiol 2023; 601:4227-4241. [PMID: 37747358 PMCID: PMC10764149 DOI: 10.1113/jp282696] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/06/2023] [Indexed: 09/26/2023] Open
Abstract
Cells execute specific responses to diverse environmental cues by encoding information in distinctly compartmentalized biochemical signalling reactions. Genetically encoded fluorescent biosensors enable the spatial and temporal monitoring of signalling events in live cells. Temporal and spatiotemporal computational models can be used to interpret biosensor experiments in complex biochemical networks and to explore hypotheses that are difficult to test experimentally. In this review, we first provide brief discussions of the experimental toolkit of fluorescent biosensors as well as computational basics with a focus on temporal and spatiotemporal deterministic models. We then describe how we used this combined approach to identify and investigate a protein kinase A (PKA) - cAMP - Ca2+ oscillatory circuit in MIN6 β cells, a mouse pancreatic β cell system. We describe the application of this combined approach to interrogate how this oscillatory circuit is differentially regulated in a nano-compartment formed at the plasma membrane by the scaffolding protein A kinase anchoring protein 79/150. We leveraged both temporal and spatiotemporal deterministic models to identify the key regulators of this oscillatory circuit, which we confirmed with further experiments. The powerful approach of combining live-cell biosensor imaging with quantitative modelling, as discussed here, should find widespread use in the investigation of spatiotemporal regulation of cell signalling.
Collapse
Affiliation(s)
- Clara Posner
- Department of Pharmacology, University of California, San Diego, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| |
Collapse
|
15
|
Weiss AM, Lopez MA, Rawe BW, Manna S, Chen Q, Mulder EJ, Rowan SJ, Esser-Kahn AP. Understanding How Cationic Polymers' Properties Inform Toxic or Immunogenic Responses via Parametric Analysis. Macromolecules 2023; 56:7286-7299. [PMID: 37781211 PMCID: PMC10537447 DOI: 10.1021/acs.macromol.3c01223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/16/2023] [Indexed: 10/03/2023]
Abstract
Cationic polymers are widely used materials in diverse biotechnologies. Subtle variations in these polymers' properties can change them from exceptional delivery agents to toxic inflammatory hazards. Conventional screening strategies optimize for function in a specific application rather than observing how underlying polymer-cell interactions emerge from polymers' properties. An alternative approach is to map basic underlying responses, such as immunogenicity or toxicity, as a function of basic physicochemical parameters to inform the design of materials for a breadth of applications. To demonstrate the potential of this approach, we synthesized 107 polymers varied in charge, hydrophobicity, and molecular weight. We then screened this library for cytotoxic behavior and immunogenic responses to map how these physicochemical properties inform polymer-cell interactions. We identify three compositional regions of interest and use confocal microscopy to uncover the mechanisms behind the observed responses. Finally, immunogenic activity is confirmed in vivo. Highly cationic polymers disrupted the cellular plasma membrane to induce a toxic phenotype, while high molecular weight, hydrophobic polymers were uptaken by active transport to induce NLRP3 inflammasome activation, an immunogenic phenotype. Tertiary amine- and triethylene glycol-containing polymers did not invoke immunogenic or toxic responses. The framework described herein allows for the systematic characterization of new cationic materials with different physicochemical properties for applications ranging from drug and gene delivery to antimicrobial coatings and tissue scaffolds.
Collapse
Affiliation(s)
- Adam M. Weiss
- Pritzker
School of Molecular Engineering, University
of Chicago, 5640 S Ellis Ave., Chicago, Illinois 60637, United States
- Department
of Chemistry, University of Chicago, 5735 S Ellis Ave., Chicago, Illinois 60637, United States
| | - Marcos A. Lopez
- Department
of Chemistry, University of Chicago, 5735 S Ellis Ave., Chicago, Illinois 60637, United States
| | - Benjamin W. Rawe
- Pritzker
School of Molecular Engineering, University
of Chicago, 5640 S Ellis Ave., Chicago, Illinois 60637, United States
| | - Saikat Manna
- Pritzker
School of Molecular Engineering, University
of Chicago, 5640 S Ellis Ave., Chicago, Illinois 60637, United States
| | - Qing Chen
- Pritzker
School of Molecular Engineering, University
of Chicago, 5640 S Ellis Ave., Chicago, Illinois 60637, United States
| | - Elizabeth J. Mulder
- Pritzker
School of Molecular Engineering, University
of Chicago, 5640 S Ellis Ave., Chicago, Illinois 60637, United States
| | - Stuart J. Rowan
- Pritzker
School of Molecular Engineering, University
of Chicago, 5640 S Ellis Ave., Chicago, Illinois 60637, United States
- Department
of Chemistry, University of Chicago, 5735 S Ellis Ave., Chicago, Illinois 60637, United States
| | - Aaron P. Esser-Kahn
- Pritzker
School of Molecular Engineering, University
of Chicago, 5640 S Ellis Ave., Chicago, Illinois 60637, United States
| |
Collapse
|
16
|
Lo CH, Zeng J. Defective lysosomal acidification: a new prognostic marker and therapeutic target for neurodegenerative diseases. Transl Neurodegener 2023; 12:29. [PMID: 37287072 PMCID: PMC10249214 DOI: 10.1186/s40035-023-00362-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/12/2023] [Indexed: 06/09/2023] Open
Abstract
Lysosomal acidification dysfunction has been implicated as a key driving factor in the pathogenesis of neurodegenerative diseases, including Alzheimer's disease and Parkinson's disease. Multiple genetic factors have been linked to lysosomal de-acidification through impairing the vacuolar-type ATPase and ion channels on the organelle membrane. Similar lysosomal abnormalities are also present in sporadic forms of neurodegeneration, although the underlying pathogenic mechanisms are unclear and remain to be investigated. Importantly, recent studies have revealed early occurrence of lysosomal acidification impairment before the onset of neurodegeneration and late-stage pathology. However, there is a lack of methods for organelle pH monitoring in vivo and a dearth of lysosome-acidifying therapeutic agents. Here, we summarize and present evidence for the notion of defective lysosomal acidification as an early indicator of neurodegeneration and urge the critical need for technological advancement in developing tools for lysosomal pH monitoring and detection both in vivo and for clinical applications. We further discuss current preclinical pharmacological agents that modulate lysosomal acidification, including small molecules and nanomedicine, and their potential clinical translation into lysosome-targeting therapies. Both timely detection of lysosomal dysfunction and development of therapeutics that restore lysosomal function represent paradigm shifts in targeting neurodegenerative diseases.
Collapse
Affiliation(s)
- Chih Hung Lo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore.
| | - Jialiu Zeng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore.
| |
Collapse
|
17
|
Van Acker ZP, Perdok A, Hellemans R, North K, Vorsters I, Cappel C, Dehairs J, Swinnen JV, Sannerud R, Bretou M, Damme M, Annaert W. Phospholipase D3 degrades mitochondrial DNA to regulate nucleotide signaling and APP metabolism. Nat Commun 2023; 14:2847. [PMID: 37225734 DOI: 10.1038/s41467-023-38501-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 05/04/2023] [Indexed: 05/26/2023] Open
Abstract
Phospholipase D3 (PLD3) polymorphisms are linked to late-onset Alzheimer's disease (LOAD). Being a lysosomal 5'-3' exonuclease, its neuronal substrates remained unknown as well as how a defective lysosomal nucleotide catabolism connects to AD-proteinopathy. We identified mitochondrial DNA (mtDNA) as a major physiological substrate and show its manifest build-up in lysosomes of PLD3-defective cells. mtDNA accretion creates a degradative (proteolytic) bottleneck that presents at the ultrastructural level as a marked abundance of multilamellar bodies, often containing mitochondrial remnants, which correlates with increased PINK1-dependent mitophagy. Lysosomal leakage of mtDNA to the cytosol activates cGAS-STING signaling that upregulates autophagy and induces amyloid precursor C-terminal fragment (APP-CTF) and cholesterol accumulation. STING inhibition largely normalizes APP-CTF levels, whereas an APP knockout in PLD3-deficient backgrounds lowers STING activation and normalizes cholesterol biosynthesis. Collectively, we demonstrate molecular cross-talks through feedforward loops between lysosomal nucleotide turnover, cGAS-STING and APP metabolism that, when dysregulated, result in neuronal endolysosomal demise as observed in LOAD.
Collapse
Affiliation(s)
- Zoë P Van Acker
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Anika Perdok
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Ruben Hellemans
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Katherine North
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Inge Vorsters
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Cedric Cappel
- Laboratory for Molecular Cell Biology and Transgenic Research, Institute of Biochemistry, Christian-Albrechts-University Kiel, Otto-Hahn-Platz 9, Kiel, Germany
| | - Jonas Dehairs
- Laboratory of Lipid Metabolism & Cancer, Department of Oncology, KU Leuven, B-3000, Leuven, Belgium
| | - Johannes V Swinnen
- Laboratory of Lipid Metabolism & Cancer, Department of Oncology, KU Leuven, B-3000, Leuven, Belgium
| | - Ragna Sannerud
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Marine Bretou
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Markus Damme
- Laboratory for Molecular Cell Biology and Transgenic Research, Institute of Biochemistry, Christian-Albrechts-University Kiel, Otto-Hahn-Platz 9, Kiel, Germany
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium.
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium.
| |
Collapse
|
18
|
Zuo Y, Chai Y, Liu X, Gao Z, Jin X, Wang F, Bai Y, Zheng Z. A ratiometric fluorescent probe based on spiropyran in situ switching for tracking dynamic changes of lysosomal autophagy and anticounterfeiting. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 291:122338. [PMID: 36657288 DOI: 10.1016/j.saa.2023.122338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/28/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Autophagy is the controlled breakdown of cellular components that dysfunctional or nonessential, and the decomposition products are further recycled and synthesized for the normal physiological activities of cells. Lysosomal autophagy has been implicated in cancer, neurological disorders, Parkinson's disease, etc. Therefore, it is necessary to develop a fluorescent probe that can clearly describe the process of lysosomal autophagy. However, there are currently limited fluorescent probes for ratiometric monitoring of the autophagic process in dual channels. To solve this problem, a fluorescent probe based on spiropyran with lysosomal targeting and pH response for ratiometric monitoring the autophagy process of lysosomes were designed. The sensitive response of the probe to pH in vitro was verified by UV and fluorescence spectrum tests. Meanwhile, the probe demonstrated the ability to monitor the intracellular pH fluctuations. In addition, the application of Lyso-SD in the field of anti-counterfeiting has been proposed based on the obvious photoluminescence ability of Lyso-SD under UV irradiation.
Collapse
Affiliation(s)
- Yujing Zuo
- Tianjin Key Laboratory of Composite & Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin 300072, China; Ningbo Yinzhou Chinaust Automobile Fittings Corp. Ltd., Ningbo 315142, China
| | - Yanfu Chai
- Tianjin Key Laboratory of Composite & Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin 300072, China; School of Mechanical and Electrical Engineering, Shaoxing University, Shaoxing 312000, China; Ningbo Yinzhou Chinaust Automobile Fittings Corp. Ltd., Ningbo 315142, China.
| | - Xiaofei Liu
- Tianjin Key Laboratory of Composite & Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Zhiming Gao
- Tianjin Key Laboratory of Composite & Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Xiaofeng Jin
- Ningbo Yinzhou Chinaust Automobile Fittings Corp. Ltd., Ningbo 315142, China
| | - Feng Wang
- Ningbo Yinzhou Chinaust Automobile Fittings Corp. Ltd., Ningbo 315142, China
| | - Yongjie Bai
- Ningbo Yinzhou Chinaust Automobile Fittings Corp. Ltd., Ningbo 315142, China
| | - Zhijun Zheng
- Ningbo Yinzhou Chinaust Automobile Fittings Corp. Ltd., Ningbo 315142, China
| |
Collapse
|
19
|
Wahl-Schott C, Freichel M, Hennis K, Philippaert K, Ottenheijm R, Tsvilovskyy V, Varbanov H. Characterization of Endo-Lysosomal Cation Channels Using Calcium Imaging. Handb Exp Pharmacol 2023; 278:277-304. [PMID: 36894791 DOI: 10.1007/164_2023_637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Endo-lysosomes are membrane-bound acidic organelles that are involved in endocytosis, recycling, and degradation of extracellular and intracellular material. The membranes of endo-lysosomes express several Ca2+-permeable cation ion channels, including two-pore channels (TPC1-3) and transient receptor potential mucolipin channels (TRPML1-3). In this chapter, we will describe four different state-of-the-art Ca2+ imaging approaches, which are well-suited to investigate the function of endo-lysosomal cation channels. These techniques include (1) global cytosolic Ca2+ measurements, (2) peri-endo-lysosomal Ca2+ imaging using genetically encoded Ca2+ sensors that are directed to the cytosolic endo-lysosomal membrane surface, (3) Ca2+ imaging of endo-lysosomal cation channels, which are engineered in order to redirect them to the plasma membrane in combination with approaches 1 and 2, and (4) Ca2+ imaging by directing Ca2+ indicators to the endo-lysosomal lumen. Moreover, we will review useful small molecules, which can be used as valuable tools for endo-lysosomal Ca2+ imaging. Rather than providing complete protocols, we will discuss specific methodological issues related to endo-lysosomal Ca2+ imaging.
Collapse
Affiliation(s)
- Christian Wahl-Schott
- Institut für Kardiovaskuläre Physiologie und Pathophysiologie, Lehrstuhl für Vegetative Physiologie, Biomedizinisches Zentrum, Ludwig-Maximilians-Universität München, München, Germany.
| | - Marc Freichel
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany. .,DZHK (German Centre for Cardiovascular Research), Heidelberg/Mannheim, Germany.
| | - Konstantin Hennis
- Institut für Kardiovaskuläre Physiologie und Pathophysiologie, Lehrstuhl für Vegetative Physiologie, Biomedizinisches Zentrum, Ludwig-Maximilians-Universität München, München, Germany
| | - Koenraad Philippaert
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg/Mannheim, Germany
| | - Roger Ottenheijm
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg/Mannheim, Germany
| | - Volodymyr Tsvilovskyy
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Heidelberg/Mannheim, Germany
| | - Hristo Varbanov
- Institut für Neurophysiologie, Medizinische Hochschule Hannover(MHH), Hannover, Germany
| |
Collapse
|
20
|
Zaver SA, Johnson CJ, Berndt A, Simpson CL. Live Imaging with Genetically Encoded Physiologic Sensors and Optogenetic Tools. J Invest Dermatol 2023; 143:353-361.e4. [PMID: 36822769 PMCID: PMC9972253 DOI: 10.1016/j.jid.2022.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/03/2022] [Accepted: 12/04/2022] [Indexed: 02/24/2023]
Abstract
Barrier tissues such as the epidermis employ complex signal transduction systems to execute morphogenetic programs and to rapidly respond to environmental cues to promote homeostasis. Recent advances in live-imaging techniques and tools allow precise spatial and temporal monitoring and manipulation of intracellular signaling cascades. Leveraging the chemistry of naturally occurring light-sensitive proteins, genetically encoded fluorescent biosensors have emerged as robust tools for visualizing dynamic signaling events. In contrast, optogenetic protein constructs permit laser-mediated control of signal receptors and effectors within live cells, organoids, and even model organisms. In this paper, we review the basic principles underlying novel biosensors and optogenetic tools and highlight how recent studies in cutaneous biology have leveraged these imaging strategies to illuminate the spatiotemporal signals regulating epidermal development, barrier formation, and tissue homeostasis.
Collapse
Affiliation(s)
- Shivam A Zaver
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington, USA; Medical Scientist Training Program, University of Washington, Seattle, Washington, USA
| | - Christopher J Johnson
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Andre Berndt
- Department of Bioengineering, University of Washington, Seattle, Washington, USA; Institute for Stem Cell and Regenerative Medicine (ISCRM), University of Washington, Seattle, Washington, USA
| | - Cory L Simpson
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington, USA; Institute for Stem Cell and Regenerative Medicine (ISCRM), University of Washington, Seattle, Washington, USA.
| |
Collapse
|
21
|
Mukherjee A, Saha PC, Kar S, Guha P, Das RS, Bera T, Guha S. Acidic pH-Triggered Live-Cell Lysosome Specific Tracking, Ratiometric pH Sensing, and Multicolor Imaging by Visible to NIR Switchable Cy-7 Dyes. Chembiochem 2023; 24:e202200641. [PMID: 36459158 DOI: 10.1002/cbic.202200641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/28/2022] [Accepted: 12/02/2022] [Indexed: 12/05/2022]
Abstract
We have demonstrated an efficient synthetic route with crystal structures for the construction of acidic pH-triggered visible-to-NIR interchangeable ratiometric fluorescent pH sensors. This bioresponsive probe exhibits pH-sensitive reversible absorption/emission features, low cytotoxicity, a huge 322 nm bathochromic spectral shift with augmented quantum yield from neutral to acidic pH, high sensitivity and selective targeting ability of live-cell lysosomes with ideal pKa , off-to-on narrow NIR absorption/fluorescence signals with high molar absorption coefficient at acidic lysosomal lumen, and in-situ live-cell pH-activated ratiometric imaging of lysosomal pH. Selective staining and ratiometric pH imaging in human carcinoma live-cell lysosomes were monitored by dual-channel confocal laser scanning microscope using a pH-activatable organic fluorescent dye comprising a morpholine moiety for lysosome targeting and an acidic pH openable oxazolidine ring. Moreover, real-time tracking of lysosomes, 3D, and multicolor live-cell imaging have been achieved using the synthesized pH-activatable probe.
Collapse
Affiliation(s)
- Ayan Mukherjee
- Department of Chemistry, Organic Chemistry Section, Jadavpur University, Kolkata, 700032, India
| | - Pranab Chandra Saha
- Department of Chemistry, Organic Chemistry Section, Jadavpur University, Kolkata, 700032, India
| | - Samiran Kar
- Department of Chemistry, Organic Chemistry Section, Jadavpur University, Kolkata, 700032, India
| | - Pampa Guha
- Department of Chemistry, City College, 102/1 Raja Rammohan Sarani, Kolkata, 700009, India
| | - Rabi Sankar Das
- Department of Chemistry, Organic Chemistry Section, Jadavpur University, Kolkata, 700032, India
| | - Tapas Bera
- Department of Chemistry, Organic Chemistry Section, Jadavpur University, Kolkata, 700032, India
| | - Samit Guha
- Department of Chemistry, Organic Chemistry Section, Jadavpur University, Kolkata, 700032, India
| |
Collapse
|
22
|
Mulligan RJ, Yap CC, Winckler B. Endosomal Transport to Lysosomes and the Trans-Golgi Network in Neurons and Other Cells: Visualizing Maturational Flux. Methods Mol Biol 2023; 2557:595-618. [PMID: 36512240 DOI: 10.1007/978-1-0716-2639-9_36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
High-level microscopy enables the comprehensive study of dynamic intracellular processes. Here we describe a toolkit of combinatorial approaches for fixed cell imaging and live cell imaging to investigate the interactions along the trans-Golgi network (TGN)-endosome-lysosome transport axis, which underlie the maturation of endosomal compartments and degradative flux. For fixed cell approaches, we specifically highlight how choices of permeabilization conditions, antibody selection, and antibody multiplexing affect interpretation of results. For live cell approaches, we emphasize the use of sensors that read out pH and degradative capacity in combination with endosomal identity for elucidating dynamic compartment changes.
Collapse
Affiliation(s)
| | - Chan Choo Yap
- Department of Cell Biology, University of Virginia, Charlottesville, VA, USA.
| | - Bettina Winckler
- Department of Cell Biology, University of Virginia, Charlottesville, VA, USA.
| |
Collapse
|
23
|
Rennick JJ, Nowell CJ, Pouton CW, Johnston APR. Resolving subcellular pH with a quantitative fluorescent lifetime biosensor. Nat Commun 2022; 13:6023. [PMID: 36224168 PMCID: PMC9556823 DOI: 10.1038/s41467-022-33348-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 09/13/2022] [Indexed: 11/24/2022] Open
Abstract
Changes in sub-cellular pH play a key role in metabolism, membrane transport, and triggering cargo release from therapeutic delivery systems. Most methods to measure pH rely on intensity changes of pH sensitive fluorophores, however, these measurements are hampered by high uncertainty in the inferred pH and the need for multiple fluorophores. To address this, here we combine pH dependant fluorescent lifetime imaging microscopy (pHLIM) with deep learning to accurately quantify sub-cellular pH in individual vesicles. We engineer the pH sensitive protein mApple to localise in the cytosol, endosomes, and lysosomes, and demonstrate that pHLIM can rapidly detect pH changes induced by drugs such as bafilomycin A1 and chloroquine. We also demonstrate that polyethylenimine (a common transfection reagent) does not exhibit a proton sponge effect and had no measurable impact on the pH of endocytic vesicles. pHLIM is a simple and quantitative method that will help to understand drug action and disease progression.
Collapse
Affiliation(s)
- Joshua J Rennick
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Cameron J Nowell
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Colin W Pouton
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Angus P R Johnston
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
| |
Collapse
|
24
|
Koda K, Keller S, Kojima R, Kamiya M, Urano Y. Measuring the pH of Acidic Vesicles in Live Cells with an Optimized Fluorescence Lifetime Imaging Probe. Anal Chem 2022; 94:11264-11271. [PMID: 35913787 DOI: 10.1021/acs.analchem.2c01840] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Acidification of intracellular vesicles, such as endosomes and lysosomes, is a key pathway for regulating the function of internal proteins. Most conventional methods of measuring pH are not satisfactory for quantifying the pH inside these vesicles. Here, we investigated the molecular requirements for a fluorescence probe to measure the intravesicular acidic pH in living cells by means of fluorescence lifetime imaging microscopy (FLIM). The developed probe, m-DiMeNAF488, exhibits a pH-dependent equilibrium between highly fluorescent and moderately fluorescent forms, which has distinct and detectable fluorescence lifetimes of 4.36 and 0.58 ns, respectively. The pKa(τ) value of m-DiMeNAF488 was determined to be 4.58, which would be favorable for evaluating the pH in the acidic vesicles. We were able to monitor the pH changes in phagosomes during phagocytosis by means of FLIM using m-DiMeNAF488. This probe is expected to be a useful tool for investigating acidic pH-regulated biological phenomena.
Collapse
Affiliation(s)
| | | | - Ryosuke Kojima
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Mako Kamiya
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Yasuteru Urano
- AMED-CREST, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| |
Collapse
|
25
|
Langeh U, Kumar V, Kumar A, Kumar P, Singh C, Singh A. Cellular and mitochondrial quality control mechanisms in maintaining homeostasis in ageing. Rejuvenation Res 2022; 25:208-222. [PMID: 35850516 DOI: 10.1089/rej.2022.0027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Aging is a natural process in all living organisms defined as destruction of cell function as a result of long-term accumulation of damages. Autophagy is a cellular house safeguard pathway which responsible for degrading damaged cellular organelles. Moreover, it maintains cellular homeostasis, control lifetime, and longevity. Damaged mitochondrial accumulation is a characteristic of aging which associated with neurodegeneration. Mitochondria functions as a principal energy source via supplying ATP through oxidative phosphorylation which serves as fuel for neuronal function. Mitophagy and mitochondrial specific autophagy plays an important role in maintenance of neuronal health via the removal of dysfunctional and aged mitochondria. The mitochondrial QC system involves different strategies for protecting against mitochondrial dysfunction and maintaining healthy mitochondria in cells. Mitochondrial function protection could be a strategy for the promotion of neuroprotection. Mitophagy, could be an effective target for drug discovery. Therefore, further detailed studies for mechanism of mitophagy will advance our mitochondrial phenotype knowledge and understanding to disease pathogenesis. This review mainly focuses on ageing mediated mechanism of autophagy and mitophagy for maintaining the cellular homeostasis and longevity.
Collapse
Affiliation(s)
- Urvashi Langeh
- ISF College of Pharmacy, 75126, Pharmacology, Moga, Punjab, India;
| | - Vishal Kumar
- ISF College of Pharmacy, 75126, Pharmacology, Moga, Punjab, India;
| | | | - Pradeep Kumar
- University of the Witwatersrand, 37707, Department of Pharmacy and Pharmacology, Johannesburg-Braamfontein, Gauteng, South Africa;
| | - Charan Singh
- ISF College of Pharmacy, 75126, Pharmacology, Moga, Punjab, India;
| | - Arti Singh
- ISF College of Pharmacy, 75126, Pharmacology, ISF College of Pharmacy, Department of Pharmacology, Moga, Moga, Punjab, India, 142001;
| |
Collapse
|
26
|
Chen PJ, Li Y, Lee CH. Calcium Imaging of Neural Activity in Fly Photoreceptors. Cold Spring Harb Protoc 2022; 2022:Pdb.top107800. [PMID: 35641092 DOI: 10.1101/pdb.top107800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Functional imaging methodologies allow researchers to simultaneously monitor the neural activities of all single neurons in a population, and this ability has led to great advances in neuroscience research. Taking advantage of a genetically tractable model organism, functional imaging in Drosophila provides opportunities to probe scientific questions that were previously unanswerable by electrophysiological recordings. Here, we introduce comprehensive protocols for two-photon calcium imaging in fly visual neurons. We also discuss some challenges in applying optical imaging techniques to study visual systems and consider the best practices for making comparisons between different neuron groups.
Collapse
Affiliation(s)
- Pei-Ju Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan, Republic of China
| | - Yan Li
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan, Republic of China
| | - Chi-Hon Lee
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan, Republic of China
| |
Collapse
|
27
|
Chin M, Ang KH, Davies J, Alquezar C, Garda VG, Rooney B, Leng K, Kampmann M, Arkin MR, Kao AW. Phenotypic Screening Using High-Content Imaging to Identify Lysosomal pH Modulators in a Neuronal Cell Model. ACS Chem Neurosci 2022; 13:1505-1516. [PMID: 35522480 PMCID: PMC9121341 DOI: 10.1021/acschemneuro.1c00804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/25/2022] [Indexed: 11/29/2022] Open
Abstract
Lysosomes are intracellular organelles responsible for the degradation of diverse macromolecules in a cell. A highly acidic pH is required for the optimal functioning of lysosomal enzymes. Loss of lysosomal intralumenal acidity can disrupt cellular protein homeostasis and is linked to age-related diseases such as neurodegeneration. Using a new robust lysosomal pH biosensor (FIRE-pHLy), we developed a cell-based fluorescence assay for high-throughput screening (HTS) and applied it to differentiated SH-SY5Y neuroblastoma cells. The goal of this study was twofold: (1) to screen for small molecules that acidify lysosomal pH and (2) to identify molecular targets and pathways that regulate lysosomal pH. We conducted a screen of 1835 bioactive compounds with annotated target information to identify lysosomal pH modulators (both acidifiers and alkalinizers). Forty-five compounds passed the initial hit selection criteria, using a combined analysis approach of population-based and object-based data. Twenty-three compounds were retested in dose-response assays and two compounds, OSI-027 and PP242, were identified as top acidifying hits. Overall, data from this phenotypic HTS screen may be used to explore novel regulatory pathways of lysosomal pH regulation. Additionally, OSI-027 and PP242 may serve as useful tool compounds to enable mechanistic studies of autophagy activation and lysosomal acidification as potential therapeutic pathways for neurodegenerative diseases.
Collapse
Affiliation(s)
- Marcus
Y. Chin
- Memory
and Aging Center, Department of Neurology, University of California, San
Francisco, California, California 94158, United States
- Small
Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Kean-Hooi Ang
- Small
Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Julia Davies
- Small
Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Carolina Alquezar
- Memory
and Aging Center, Department of Neurology, University of California, San
Francisco, California, California 94158, United States
| | - Virginia G. Garda
- Memory
and Aging Center, Department of Neurology, University of California, San
Francisco, California, California 94158, United States
- Small
Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Brendan Rooney
- Institute
for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, United States
| | - Kun Leng
- Institute
for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, United States
- Biomedical
Sciences Graduate Program, University of
California, San Francisco, California 94158, United States
- Medical
Scientist Training Program, University of
California, San Francisco, California 94158, United States
| | - Martin Kampmann
- Institute
for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, United States
| | - Michelle R. Arkin
- Small
Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Aimee W. Kao
- Memory
and Aging Center, Department of Neurology, University of California, San
Francisco, California, California 94158, United States
| |
Collapse
|
28
|
Barral DC, Staiano L, Guimas Almeida C, Cutler DF, Eden ER, Futter CE, Galione A, Marques ARA, Medina DL, Napolitano G, Settembre C, Vieira OV, Aerts JMFG, Atakpa‐Adaji P, Bruno G, Capuozzo A, De Leonibus E, Di Malta C, Escrevente C, Esposito A, Grumati P, Hall MJ, Teodoro RO, Lopes SS, Luzio JP, Monfregola J, Montefusco S, Platt FM, Polishchuck R, De Risi M, Sambri I, Soldati C, Seabra MC. Current methods to analyze lysosome morphology, positioning, motility and function. Traffic 2022; 23:238-269. [PMID: 35343629 PMCID: PMC9323414 DOI: 10.1111/tra.12839] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 01/09/2023]
Abstract
Since the discovery of lysosomes more than 70 years ago, much has been learned about the functions of these organelles. Lysosomes were regarded as exclusively degradative organelles, but more recent research has shown that they play essential roles in several other cellular functions, such as nutrient sensing, intracellular signalling and metabolism. Methodological advances played a key part in generating our current knowledge about the biology of this multifaceted organelle. In this review, we cover current methods used to analyze lysosome morphology, positioning, motility and function. We highlight the principles behind these methods, the methodological strategies and their advantages and limitations. To extract accurate information and avoid misinterpretations, we discuss the best strategies to identify lysosomes and assess their characteristics and functions. With this review, we aim to stimulate an increase in the quantity and quality of research on lysosomes and further ground-breaking discoveries on an organelle that continues to surprise and excite cell biologists.
Collapse
Affiliation(s)
- Duarte C. Barral
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | - Leopoldo Staiano
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Institute for Genetic and Biomedical ResearchNational Research Council (CNR)MilanItaly
| | | | - Dan F. Cutler
- MRC Laboratory for Molecular Cell BiologyUniversity College LondonLondonUK
| | - Emily R. Eden
- University College London (UCL) Institute of OphthalmologyLondonUK
| | - Clare E. Futter
- University College London (UCL) Institute of OphthalmologyLondonUK
| | | | | | - Diego Luis Medina
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | - Gennaro Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Clinical Medicine and Surgery DepartmentFederico II UniversityNaplesItaly
| | - Otília V. Vieira
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | | | | | - Gemma Bruno
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | | | - Elvira De Leonibus
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Institute of Biochemistry and Cell Biology, CNRRomeItaly
| | - Chiara Di Malta
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | | | | | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Michael J. Hall
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | - Rita O. Teodoro
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | - Susana S. Lopes
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | - J. Paul Luzio
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | | | | | | | | | - Maria De Risi
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Irene Sambri
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | - Chiara Soldati
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Miguel C. Seabra
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| |
Collapse
|
29
|
Karsten L, Goett-Zink L, Schmitz J, Hoffrogge R, Grünberger A, Kottke T, Müller KM. Genetically Encoded Ratiometric pH Sensors for the Measurement of Intra- and Extracellular pH and Internalization Rates. BIOSENSORS 2022; 12:bios12050271. [PMID: 35624572 PMCID: PMC9138566 DOI: 10.3390/bios12050271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022]
Abstract
pH-sensitive fluorescent proteins as genetically encoded pH sensors are promising tools for monitoring intra- and extracellular pH. However, there is a lack of ratiometric pH sensors, which offer a good dynamic range and can be purified and applied extracellularly to investigate uptake. In our study, the bright fluorescent protein CoGFP_V0 was C-terminally fused to the ligand epidermal growth factor (EGF) and retained its dual-excitation and dual-emission properties as a purified protein. The tandem fluorescent variants EGF-CoGFP-mTagBFP2 (pK′ = 6.6) and EGF-CoGFP-mCRISPRed (pK′ = 6.1) revealed high dynamic ranges between pH 4.0 and 7.5. Using live-cell fluorescence microscopy, both pH sensor molecules permitted the conversion of fluorescence intensity ratios to detailed intracellular pH maps, which revealed pH gradients within endocytic vesicles. Additionally, extracellular binding of the pH sensors to cells expressing the EGF receptor (EGFR) enabled the tracking of pH shifts inside cultivation chambers of a microfluidic device. Furthermore, the dual-emission properties of EGF-CoGFP-mCRISPRed upon 488 nm excitation make this pH sensor a valuable tool for ratiometric flow cytometry. This high-throughput method allowed for the determination of internalization rates, which represents a promising kinetic parameter for the in vitro characterization of protein–drug conjugates in cancer therapy.
Collapse
Affiliation(s)
- Lennard Karsten
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
| | - Lukas Goett-Zink
- Biophysical Chemistry and Diagnostics, Medical School OWL, Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany; (L.G.-Z.); (T.K.)
| | - Julian Schmitz
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (J.S.); (A.G.)
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Raimund Hoffrogge
- Cell Culture Technology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (J.S.); (A.G.)
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Tilman Kottke
- Biophysical Chemistry and Diagnostics, Medical School OWL, Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany; (L.G.-Z.); (T.K.)
| | - Kristian M. Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
- Correspondence:
| |
Collapse
|
30
|
Michelis S, Danglot L, Vauchelles R, Klymchenko AS, Collot M. Imaging and Measuring Vesicular Acidification with a Plasma Membrane-Targeted Ratiometric pH Probe. Anal Chem 2022; 94:5996-6003. [PMID: 35377610 DOI: 10.1021/acs.analchem.2c00574] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Tracking the pH variation of intracellular vesicles throughout the endocytosis pathway is of prior importance to better assess the cell trafficking and metabolism of cells. Small molecular fluorescent pH probes are valuable tools in bioimaging but are generally not targeted to intracellular vesicles or are directly targeted to acidic lysosomes, thus not allowing the dynamic observation of the vesicular acidification. Herein, we designed Mem-pH, a fluorogenic ratiometric pH probe based on chromenoquinoline with appealing photophysical properties, which targets the plasma membrane (PM) of cells and further accumulates in the intracellular vesicles by endocytosis. The exposition of Mem-pH toward the vesicle's lumen allowed to monitor the acidification of the vesicles throughout the endocytic pathway and enabled the measurement of their pH via ratiometric imaging.
Collapse
Affiliation(s)
- Sophie Michelis
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Lydia Danglot
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy & Diseased Brain, 75014 Paris, France
| | - Romain Vauchelles
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Mayeul Collot
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| |
Collapse
|
31
|
Udayar V, Chen Y, Sidransky E, Jagasia R. Lysosomal dysfunction in neurodegeneration: emerging concepts and methods. Trends Neurosci 2022; 45:184-199. [PMID: 35034773 PMCID: PMC8854344 DOI: 10.1016/j.tins.2021.12.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 11/23/2021] [Accepted: 12/12/2021] [Indexed: 02/06/2023]
Abstract
The understanding of lysosomes has come a long way since the initial discovery of their role in degrading cellular waste. The lysosome is now recognized as a highly dynamic organelle positioned at the crossroads of cell signaling, transcription, and metabolism. Underscoring its importance is the observation that, in addition to rare monogenic lysosomal storage disorders, genes regulating lysosomal function are implicated in common sporadic neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS). Developing therapies for these disorders is particularly challenging, largely due to gaps in knowledge of the underlying molecular and cellular processes. In this review, we discuss technological advances that have propelled deeper understanding of the lysosome in neurodegeneration, from elucidating the functions of lysosome-related disease risk variants at the level of the organelle, cell, and tissue, to the development of disease-specific biological models that recapitulate disease manifestations. Finally, we identify key questions to be addressed to successfully bridge the gap to the clinic.
Collapse
Affiliation(s)
- Vinod Udayar
- Roche Pharmaceutical Research and Early Development, Neuroscience and Rare Diseases Discovery & Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Yu Chen
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ellen Sidransky
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Ravi Jagasia
- Roche Pharmaceutical Research and Early Development, Neuroscience and Rare Diseases Discovery & Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| |
Collapse
|
32
|
Yapici N, Gao X, Yan X, Hou S, Jockusch S, Lesniak L, Gibson KM, Bi L. Novel Dual-Organelle-Targeting Probe (RCPP) for Simultaneous Measurement of Organellar Acidity and Alkalinity in Living Cells. ACS OMEGA 2021; 6:31447-31456. [PMID: 34869971 PMCID: PMC8637586 DOI: 10.1021/acsomega.1c03087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/01/2021] [Indexed: 05/06/2023]
Abstract
Many organelles, such as lysosomes and mitochondria, maintain a pH that is different from the cytoplasmic pH. These pH differences have important functional ramifications for those organelles. Many cellular events depend upon a well-compartmentalized distribution of H+ ions spanning the membrane for the optimal function. Cells have developed a variety of mechanisms that enable the regulation of organelle pH. However, the measurement of organellar acidity/alkalinity in living cells has remained a challenge. Currently, most existing probes for the estimation of intracellular pH show a single -organelle targeting capacity. Such probes provide data that fails to comprehensively reveal the pathological and physiological roles and connections between mitochondria and lysosomes in different species. Mitochondrial and lysosomal functions are closely related and important for regulating cellular homeostasis. Accordingly, the design of a single fluorescent probe that can simultaneously target mitochondria and lysosomes is highly desirable, enabling a better understanding of the crosstalk between these organelles. We report the development of a novel fluorescent sensor, rhodamine-coumarin pH probe (RCPP), for detection of organellar acidity/alkalinity. RCPP simultaneously moves between mitochondrion and lysosome subcellular locations, facilitating the simultaneous monitoring of pH alterations in mitochondria and lysosomes.
Collapse
Affiliation(s)
- Nazmiye
B. Yapici
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Xiang Gao
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Xin Yan
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Shanshan Hou
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Steffen Jockusch
- Department
of Chemistry, Columbia University, New York, New York 10027, United States
| | - Lillian Lesniak
- Department
of Chemical Engineering, Michigan Technological
University, Houghton, Michigan 49931, United States
| | - K. Michael Gibson
- Department
of Pharmacotherapy, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington 99202, United States
| | - Lanrong Bi
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| |
Collapse
|
33
|
Ovechkina VS, Zakian SM, Medvedev SP, Valetdinova KR. Genetically Encoded Fluorescent Biosensors for Biomedical Applications. Biomedicines 2021; 9:biomedicines9111528. [PMID: 34829757 PMCID: PMC8615007 DOI: 10.3390/biomedicines9111528] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
One of the challenges of modern biology and medicine is to visualize biomolecules in their natural environment, in real-time and in a non-invasive fashion, so as to gain insight into their physiological behavior and highlight alterations in pathological settings, which will enable to devise appropriate therapeutic strategies. Genetically encoded fluorescent biosensors constitute a class of imaging agents that enable visualization of biological processes and events directly in situ, preserving the native biological context and providing detailed insight into their localization and dynamics in cells. Real-time monitoring of drug action in a specific cellular compartment, organ, or tissue type; the ability to screen at the single-cell resolution; and the elimination of false-positive results caused by low drug bioavailability that is not detected by in vitro testing methods are a few of the obvious benefits of using genetically encoded fluorescent biosensors in drug screening. This review summarizes results of the studies that have been conducted in the last years toward the fabrication of genetically encoded fluorescent biosensors for biomedical applications with a comprehensive discussion on the challenges, future trends, and potential inputs needed for improving them.
Collapse
Affiliation(s)
- Vera S. Ovechkina
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.S.O.); (S.M.Z.); (S.P.M.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Suren M. Zakian
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.S.O.); (S.M.Z.); (S.P.M.)
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, 630055 Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Sergey P. Medvedev
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.S.O.); (S.M.Z.); (S.P.M.)
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, 630055 Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Kamila R. Valetdinova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.S.O.); (S.M.Z.); (S.P.M.)
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, 630055 Novosibirsk, Russia
- Correspondence:
| |
Collapse
|
34
|
Chin MY, Patwardhan AR, Ang KH, Wang AL, Alquezar C, Welch M, Nguyen PT, Grabe M, Molofsky AV, Arkin MR, Kao AW. Genetically Encoded, pH-Sensitive mTFP1 Biosensor for Probing Lysosomal pH. ACS Sens 2021; 6:2168-2180. [PMID: 34102054 PMCID: PMC8240087 DOI: 10.1021/acssensors.0c02318] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 04/08/2021] [Indexed: 12/15/2022]
Abstract
Lysosomes are important sites for macromolecular degradation, defined by an acidic lumenal pH of ∼4.5. To better understand lysosomal pH, we designed a novel, genetically encoded, fluorescent protein (FP)-based pH biosensor called Fluorescence Indicator REporting pH in Lysosomes (FIRE-pHLy). This biosensor was targeted to lysosomes with lysosomal-associated membrane protein 1 (LAMP1) and reported lumenal pH between 3.5 and 6.0 with monomeric teal fluorescent protein 1 (mTFP1), a bright cyan pH-sensitive FP variant with a pKa of 4.3. Ratiometric quantification was enabled with cytosolically oriented mCherry using high-content quantitative imaging. We expressed FIRE-pHLy in several cellular models and quantified the alkalinizing response to bafilomycin A1, a specific V-ATPase inhibitor. In summary, we have engineered FIRE-pHLy, a specific, robust, and versatile lysosomal pH biosensor, that has broad applications for investigating pH dynamics in aging- and lysosome-related diseases, as well as in lysosome-based drug discovery.
Collapse
Affiliation(s)
- Marcus Y Chin
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, California 94158, United States
- Small Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Anand R Patwardhan
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, California 94158, United States
| | - Kean-Hooi Ang
- Small Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Austin L Wang
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, California 94158, United States
| | - Carolina Alquezar
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, California 94158, United States
| | - Mackenzie Welch
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, California 94158, United States
| | - Phi T Nguyen
- Weill Institute for Neurosciences, Department of Psychiatry, University of California, San Francisco, California 94158, United States
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Anna V Molofsky
- Weill Institute for Neurosciences, Department of Psychiatry, University of California, San Francisco, California 94158, United States
| | - Michelle R Arkin
- Small Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Aimee W Kao
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, California 94158, United States
| |
Collapse
|